Move projectfile into subpackage refs #219

pyrs/core/nexus_conversion.py

@@ -9,9 +9,8 @@
 import os
 from pyrs.core import workspaces
 from pyrs.core.instrument_geometry import AnglerCameraDetectorGeometry, HidraSetup
-from pyrs.projectfile import HidraConstants
+from pyrs.projectfile import HidraConstants, HidraProjectFile, HidraProjectFileMode
 from pyrs.utilities import checkdatatypes
-from pyrs.utilities.rs_project_file import HidraProjectFile, HidraProjectFileMode
 
 
 class NeXusConvertingApp(object):

pyrs/core/powder_pattern.py

@@ -1,9 +1,8 @@
 from pyrs.core import reduction_manager
 from pyrs.utilities import checkdatatypes
 from pyrs.core import mask_util
-from pyrs.projectfile import HidraProjectFileMode
+from pyrs.projectfile import HidraProjectFile, HidraProjectFileMode
 from pyrs.utilities import calibration_file_io
-from pyrs.utilities.rs_project_file import HidraProjectFile
 from matplotlib import pyplot as plt
 
 

pyrs/core/pyrscore.py

@@ -3,8 +3,7 @@
 from pyrs.core import instrument_geometry
 from pyrs.utilities import file_util
 from pyrs.peaks import PeakFitEngineFactory, SupportedPeakProfiles, SupportedBackgroundTypes
-from pyrs.projectfile import HidraConstants, HidraProjectFileMode
-from pyrs.utilities.rs_project_file import HidraProjectFile
+from pyrs.projectfile import HidraConstants, HidraProjectFile, HidraProjectFileMode
 from pyrs.core import strain_stress_calculator
 from pyrs.core import reduction_manager
 from pyrs.core import polefigurecalculator

pyrs/core/reduction_manager.py

@@ -7,10 +7,9 @@
 from pyrs.core import mask_util
 from pyrs.core import reduce_hb2b_mtd
 from pyrs.core import reduce_hb2b_pyrs
-from pyrs.projectfile import HidraConstants, HidraProjectFileMode
+from pyrs.projectfile import HidraConstants, HidraProjectFile, HidraProjectFileMode
 from pyrs.utilities import calibration_file_io
 from pyrs.utilities import checkdatatypes
-from pyrs.utilities.rs_project_file import HidraProjectFile
 
 
 class HB2BReductionManager(object):

pyrs/core/workspaces.py

@@ -1,9 +1,8 @@
 # Data manager
 import numpy
 from pyrs.dataobjects import SampleLogs
-from pyrs.projectfile import HidraConstants
+from pyrs.projectfile import HidraConstants, HidraProjectFile
 from pyrs.utilities import checkdatatypes
-from pyrs.utilities import rs_project_file
 
 
 class HidraWorkspace(object):
@@ -57,7 +56,7 @@ def _load_raw_counts(self, hidra_file):
         :param hidra_file:
         :return:
         """
-        checkdatatypes.check_type('HIDRA project file', hidra_file, rs_project_file.HidraProjectFile)
+        checkdatatypes.check_type('HIDRA project file', hidra_file, HidraProjectFile)
 
         for sub_run_i in self._sample_logs.subruns:
             counts_vec_i = hidra_file.read_raw_counts(sub_run_i)
@@ -72,7 +71,7 @@ def _load_reduced_diffraction_data(self, hidra_file):
         :return:
         """
         # Check inputs
-        checkdatatypes.check_type('HIDRA project file', hidra_file, rs_project_file.HidraProjectFile)
+        checkdatatypes.check_type('HIDRA project file', hidra_file, HidraProjectFile)
 
         # get 2theta value
         try:
@@ -124,7 +123,7 @@ def _load_instrument(self, hidra_file):
         :return:
         """
         # Check
-        checkdatatypes.check_type('HIDRA project file', hidra_file, rs_project_file.HidraProjectFile)
+        checkdatatypes.check_type('HIDRA project file', hidra_file, HidraProjectFile)
 
         # Get values
         self._instrument_setup = hidra_file.read_instrument_geometry()
@@ -136,7 +135,7 @@ def _load_sample_logs(self, hidra_file):
         :param hidra_file:  HIDRA project file instance
         :return:
         """
-        checkdatatypes.check_type('HIDRA project file', hidra_file, rs_project_file.HidraProjectFile)
+        checkdatatypes.check_type('HIDRA project file', hidra_file, HidraProjectFile)
 
         # overwrite the existing sample logs
         self._sample_logs = hidra_file.read_sample_logs()
@@ -146,7 +145,7 @@ def _load_wave_length(self, hidra_file):
         :param hidra_file:  HIDRA project file instance
         :return:
         """
-        checkdatatypes.check_type('HIDRA project file', hidra_file, rs_project_file.HidraProjectFile)
+        checkdatatypes.check_type('HIDRA project file', hidra_file, HidraProjectFile)
 
         # reset the wave length (dictionary) from HIDRA project file
         self._wave_length_dict = hidra_file.read_wavelengths()
@@ -258,7 +257,7 @@ def load_hidra_project(self, hidra_file, load_raw_counts, load_reduced_diffracti
         :return:
         """
         # Check input
-        checkdatatypes.check_type('HIDRA project file', hidra_file, rs_project_file.HidraProjectFile)
+        checkdatatypes.check_type('HIDRA project file', hidra_file, HidraProjectFile)
         self._project_file_name = hidra_file.name
 
         # create the spectrum map - must exist before loading the counts array
@@ -645,7 +644,7 @@ def save_reduced_diffraction_data(self, hidra_project):
         :param hidra_project: HidraProjectFile instance
         :return:
         """
-        checkdatatypes.check_type('HIDRA project file', hidra_project, rs_project_file.HidraProjectFile)
+        checkdatatypes.check_type('HIDRA project file', hidra_project, HidraProjectFile)
 
         hidra_project.write_reduced_diffraction_data_set(self._2theta_matrix, self._diff_data_set)
 

pyrs/dataobjects.py

@@ -1,7 +1,7 @@
 # extentable version of dict https://treyhunner.com/2019/04/why-you-shouldnt-inherit-from-list-and-dict-in-python/
 from collections import MutableMapping
 import numpy as np
-from pyrs.projectfile import HidraConstants
+
 
 def _coerce_to_ndarray(value):
     if isinstance(value, np.ndarray):
@@ -11,7 +11,7 @@ def _coerce_to_ndarray(value):
 
 
 class SampleLogs(MutableMapping):
-    SUBRUN_KEY = HidraConstants.SUB_RUNS
+    SUBRUN_KEY = 'sub-runs'  # TODO should be pyrs.projectfile.HidraConstants.SUB_RUNS
 
     def __init__(self, **kwargs):
         self._data = dict(kwargs)

pyrs/peaks/peak_fit_engine.py

@@ -1,7 +1,6 @@
 # This is the virtual base class as the fitting frame
 import numpy as np
 from pyrs.core import workspaces
-from pyrs.utilities import rs_project_file
 from pyrs.core import peak_profile_utility
 from pyrs.core.peak_profile_utility import PeakShape
 from pyrs.utilities import checkdatatypes
@@ -175,22 +174,23 @@ def estimate_peak_height(self, peak_range):
 
         return peak_heights, flat_bkgds
 
-    def export_to_hydra_project(self, hydra_project_file, peak_tag):
+    def export_to_hydra_project(self, hidra_project_file, peak_tag):
         """Export fit result from this fitting engine instance to Hidra project file
 
         Parameters
         ----------
-        hydra_project_file : pyrs.utilities.rs_project_file.HidraProjectFile
+        hidra_project_file : ~pyrs.projectfile.HidraProjectFile
         peak_tag
 
         Returns
         -------
 
         """
-        # Check input
-        checkdatatypes.check_type('Hidra project file', hydra_project_file, rs_project_file.HidraProjectFile)
-
-        hydra_project_file.write_peak_fit_result(self._peak_collection_dict[peak_tag])
+        try:
+            hidra_project_file.write_peak_fit_result(self._peak_collection_dict[peak_tag])
+        except AttributeError as e:
+            print 'Parameter "hidra_project_file" does not appear to be correct type', e
+            raise RuntimeError('Method requires a HidraProjectFile')
 
     def fit_peaks(self, peak_tag, sub_run_range, peak_function_name, background_function_name, peak_center,
                   peak_range, max_chi2=1E3, max_peak_shift=2, min_intensity=None):

pyrs/projectfile/__init__.py

@@ -1,6 +1,8 @@
 # flake8: noqa
-# pylint: disable=undefined-variable
-from .constants import HidraConstants
-from .file_mode import HidraProjectFileMode
+from __future__ import (absolute_import, division, print_function)  # python3 compatibility
 
-__all__ = constants.__all__ + file_mode.__all__
+from .constants import *
+from .file_mode import *
+from .file_object import *
+
+__all__ = constants.__all__ + file_mode.__all__ + file_object.__all__

pyrs/utilities/rs_project_file.py → pyrs/projectfile/file_object.py

@@ -10,7 +10,7 @@
 from pyrs.dataobjects import SampleLogs
 from pyrs.projectfile import HidraConstants, HidraProjectFileMode
 
-__all__ = ['DiffractionUnit', 'HidraProjectFile']
+__all__ = ['HidraProjectFile']
 
 
 class DiffractionUnit(Enum):

scripts/preparetest/convert_hb2b_peaks.py

@@ -9,7 +9,7 @@
 """
 import numpy
 from pyrs.utilities import rs_scan_io
-from pyrs.utilities.rs_project_file import HidraProjectFile
+from pyrs.projectfile import HidraProjectFile
 
 
 def main():

scripts/preparetest/convert_hzb_data.py

@@ -11,11 +11,11 @@
 1. Add PyRS path to python path (refer to pyrsdev.sh)
 2. Run this script
 """
+import numpy
 import os
 from pyrs.core.instrument_geometry import HidraSetup
+from pyrs.projectfile import HidraConstants, HidraProjectFile, HidraProjectFileMode
 from pyrs.utilities import file_util
-from pyrs.utilities.rs_project_file import HidraConstants, HidraProjectFile, HidraProjectFileMode
-import numpy
 
 
 def parse_hzb_tiff(tiff_file_name):

scripts/preparetest/convert_strain_stress_data.py

@@ -2,8 +2,7 @@
 # System (library) test for classes and methods that will be used to calculate strain and stress
 import os
 import sys
-from pyrs.projectfile import HidraProjectFileMode
-from pyrs.utilities.rs_project_file import HidraProjectFile
+from pyrs.projectfile import HidraProjectFile, HidraProjectFileMode
 
 
 def contain_strain_stress_main():

scripts/pyrs_calibration.py

@@ -1,8 +1,7 @@
 import numpy
 import time
-from pyrs.projectfile import HidraProjectFileMode
+from pyrs.projectfile import HidraProjectFile, HidraProjectFileMode
 from pyrs.utilities import calibration_file_io
-from pyrs.utilities.rs_project_file import HidraProjectFile
 from pyrs.calibration import peakfit_calibration
 
 # DEFAULT VALUES FOR DATA PROCESSING

tests/integration/test_calibration_class.py

@@ -5,9 +5,8 @@
 import time
 import os
 import json
-from pyrs.projectfile import HidraProjectFileMode
+from pyrs.projectfile import HidraProjectFile, HidraProjectFileMode
 from pyrs.utilities import calibration_file_io
-from pyrs.utilities.rs_project_file import HidraProjectFile
 try:
     from pyrs.calibration import peakfit_calibration
 except ImportError as e:

tests/integration/test_peak_fitting.py

@@ -6,7 +6,7 @@
 from pyrs.core.peak_profile_utility import PeakShape, BackgroundFunction
 from pyrs.core.summary_generator import SummaryGenerator
 from pyrs.dataobjects import SampleLogs
-from pyrs.utilities.rs_project_file import HidraProjectFile
+from pyrs.projectfile import HidraProjectFile
 from pyrs.peaks import PeakFitEngineFactory
 import h5py
 from pyrs.core import peak_profile_utility

tests/integration/test_project_file_rw.py

@@ -1,5 +1,5 @@
 from pyrs.core import workspaces
-from pyrs.utilities.rs_project_file import HidraProjectFile
+from pyrs.projectfile import HidraProjectFile
 from pyrs.core.instrument_geometry import HidraSetup
 import os
 import pytest

tests/integration/test_reduction.py

@@ -1,4 +1,4 @@
-from pyrs.utilities.rs_project_file import HidraProjectFile
+from pyrs.projectfile import HidraProjectFile
 from pyrs.utilities import calibration_file_io
 from pyrs.core import workspaces
 import pytest

tests/unit/test_hidra_project_file.py

@@ -1,8 +1,7 @@
 """
 Test for reading and writing components to HiDRA project file
 """
-from pyrs.projectfile import HidraConstants, HidraProjectFileMode
-from pyrs.utilities.rs_project_file import HidraProjectFile
+from pyrs.projectfile import HidraConstants, HidraProjectFile, HidraProjectFileMode
 import os
 import numpy as np
 import datetime